Variant report

Variant	rs13000793
Chromosome Location	chr2:86189720-86189721
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86187922..86190334-chr2:86421070..86423340,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10181091	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181916	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10183118	0.84[EUR][1000 genomes]
rs10186005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189191	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10198260	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1020095	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11890514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891625	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12470643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472588	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476390	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12714161	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12714163	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714164	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12714165	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13397189	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1438153	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1438155	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1561330	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1866242	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866243	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1866245	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278536	0.81[CHD][hapmap]
rs4346389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4480982	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4514874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832018	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832020	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6547651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6706720	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713002	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728146	0.81[EUR][1000 genomes]
rs6737454	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6740044	0.81[CHD][hapmap]
rs7597264	0.86[ASN][1000 genomes]
rs934830	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13000793	MRPL35	cis	cerebellum	SCAN
rs13000793	IMMT	cis	lymphoblastoid	seeQTL
rs13000793	C2orf51	cis	cerebellum	SCAN
rs13000793	IMMT	cis	uninvolved skin	skin_eQTL
rs13000793	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs13000793	REEP1	cis	parietal	SCAN
rs13000793	IMMT	cis	cerebellum	SCAN
rs13000793	PTCD3	cis	cerebellum	SCAN
rs13000793	MRPL35	cis	parietal	SCAN
rs13000793	ST3GAL5	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86183800-86190800	Weak transcription	Stomach Mucosa	stomach
2	chr2:86189600-86190200	Weak transcription	A549	lung

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